Pectic polysaccharides modulate gut fermentation ability, which is determined by structural characteristics. In this work, apple pectins were extracted by HCl (HAEP), NaOH (AEP), cellulase (EAEP), and in parallel cell wall pectic fractions were sequentially extracted by water (WEP), chelator (CEP) and NaOH (NEP). The aim is to comprehensively compare the impact of extraction on pectin structure and gut fermentation behavior. Results showed that high content of galacturonic acid (90.65 mol%) and large molecular weight (675 kg/mol) were detected in the HAEP. Molecular morphology of the HAEP presented high linearity, while AEP, EAEP and WEP exhibited compact filamentous structures with highly branched patterns. The AEP was characterized by high yield (33.1 g/100 g d.b.), moderate molecular weight (304 kg/mol) and large extent of rhamnogalacturonan-I region (24.88 %) with low degree of branching (1.77). After in vitro simulated gut fermentation for 24 h, total content of short-chain fatty acid (SCFA) generated with the AEP supplement increased to 36.8 mmol/L, followed by EAEP, HAEP and WEP (25.2, 24.2 and 20.3 mmol/L, respectively). Meanwhile, WEP simultaneously produced the highest ammonia content (22.4 mmol/L). This investigation suggests that the fermentation of AEP produces more beneficial SCFA and less ammonia, thus indicating a better gut fermentation property.